Hello All, can anyone help?

Hello all, I have a 1989 GMC Jimmy 4X4 with a 5.7L. I bought it last fall from a kid that did some work to it, but I am having to go through it and double check what I can. I have put less than 100 miles on it so far, but who knows how many miles the truck has on it; The truck has ALOT of rust, especially holes in the body tub. This doesn't bother me because this is my beach/fishing truck:glasses:; so I may just glass over the holes to reinforce the floor. I do have some questions though. This truck has had a rough life. Question #1:Can I easily switch both front windows as well as the back window from power to manual? Question #2: Can I switch from solid back side windows to sliding easily? Question #3: Well, this is really an electrical issue that I am wondering if anyone else can shed some light on. I know I have a short and know how frustrating they can be. The previous owner replaced the alternator just before I bought the truck (this may be relevant, so I figured I'd mention that). I replaced the battery 5-6 weeks ago because the last one died (not to mention it was way to big to fit totally on the battery tray, and it was held in with a bungee cord and looked like they found it in a junk yard. Then I started the truck last week after it had been sitting a week or two. It sounded like it was a bit slow to start, but I figured it was since it had been sitting for a bit. I drove it about 5 miles to my destination. When I came out the battery was dead and the truck would only "click" when trying to start the truck. I got a jump and began to drive home; after about 4 miles I was driving at 50 mph and everything electrical in the truck INSTANTLY died as well as the engine. After that nothing electrical would respond. After about 15-20 minutes it went back to "clicking" when the key was turned. The weird thing was that I could hear the fuel pump running the ENTIRE time (except when the key was being held in the "start" position); even when I turned the ignition off and removed the key the fuel pump would keep running, so I disconnected the positive lead from the battery. After being towed the last mile back home, I began to look closely at the wires under the hood. I taped up 5 or 6 wires that had copper showing and could have shorted to something; and charged the battery, fastened it in better than a bungee cord and put some insulator caps on the battery posts since the previous owner switched it to a top post battery (just incase it was arcing to the hood or top radiator cross member). I also fixed a wire that the previous owner had tried to fix but the butt connector came right off with a slight bump. This was a wire that connects to the top of the alternator. The connector that has 3 wires, but only one is used. The truck started fine but I have only had a chance to drive it a hundred yards or so. Long story short, I have fixed what I could see, but does the fuel pump running constantly like that sound familiar to anyone? Would that symptom narrow the cause to something I have not yet thought about? Question #4: Does anyone make something like a floor pan / floor board liner or insert that can be glued in to seal rust holes? Sorry to be long winded, but I wanted to give as much info as possible. If anyone knows any of these answers, I would greatly appreciate it (especially questions 3 and 1).